Preheat oven to 400 degrees . Brush the inner flesh of the squash with oil and season with salt and black pepper. Place the squash on a foil-lined baking sheet, cut side down. Cook for 30-40 minutes or until a knife can easily pierce through the skin. Allow to cool. Using a fork, run it inside scraping lengthwise to create "spaghetti" noodles.

Heat oil in a skillet over medium-high heat. Add sausage and cook for about 3 to 4 minutes, crumbling as you go to brown. Add onion, garlic and mushrooms and cook until meat is browned. Add green pepper, tomatoes, salt and pepper. Sprinkle in thyme, oregano and pepper flakes, if using. Reduce heat and simmer for 10 minutes.

Reduce heat to 350 degrees. Add the sauce on top of the prepared squash halves. Sprinkle with cheese and back for 10 minutes or until heated through and cheese is melted. Remove from oven and allow to cool for 5 minutes. Garnish with basil and serve.